Publications

Enhanced cellular longevity arising from environmental fluctuations

Yuting Liu, Zhen Zhou, Hetian Su, Songlin Wu, Gavin Ni, Alex Zhang, Lev S Tsimring, Jeff Hasty, Nan Hao
Cell Systems (2024)

Live bacterial therapeutics for detection and treatment of colorectal cancer

Joanna Zhang, Jeff Hasty, Amir Zarrinpar
Nature Reviews Gastroenterology & Hepatology (2024)

Engineered bacterial therapeutics for detecting and treating CRC

Nicole Siguenza, Arianna Brevi, Joanna T Zhang, Arman Pabani, Abhinav Bhushan, Moumita Das, Yousong Ding, Jeff Hasty, Pradipta Ghosh, Amir Zarrinpar
Trends in Cancer (2024)

Phenotypic Patterning through Copy Number Adaptation to Environmental Gradients

Paige Steppe, Camilo Rey-Bedón, Shalni Kumar, Emerald Forrest, Niklas Van Der Wagt, Arnav Tayal, Lev Tsimring, Jeff Hasty
ACS Synthetic Biology (2024)

A Standardized Set of MoClo-Compatible Inducible Promoter Systems for Tunable Gene Expression in Yeast

Richard O’Laughlin, Quoc Tran, Andrew Lezia, Wasu Ngamkanjanarat, Philip Emmanuele, Nan Hao, Jeff Hasty
ACS Synthetic Biology, 85–102 (2023)

Design of synthetic bacterial biosensors

Alyssa J Chiang, Jeff Hasty
Current Opinion in Microbiology 76, 102380 (2023)

High-resolution temporal profiling of E. coli

Arianna Miano, Kevin Rychel, Andrew Lezia, Anand Sastry, Bernhard Palsson, Jeff Hasty
Nature Communications 14,1 (2023)

Multigenerational silencing dynamics control cell aging

Yang Li, Meng Jin, Richard O’Laughlin, Philip Bittihn, Lev Tsimring, Lorraine Pillus, Jeff Hasty, and Nan Hao
Proceedings of the National Academy of Sciences, 114(42):11253-11258 (2017)

Rapid and Scalable Preparation of Bacterial Lysates for Cell-Free Gene Expression

Andriy Didovyk, Taishi Tonooka, Lev Tsimring, and Jeff Hasty
ACS Synthetic Biology, 10.1021/acssynbio.7b00253 (2017)

Synchronized DNA cycling across a bacterial population

Leo Baumgart, William Mather, Jeff Hasty
Nature Genetics, 49: 1282-1285 (2017)

A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis

Spencer R. Scott, M. Omar Din, Philip Bittihn, Liyang Xiong, Lev S. Tsimring and Jeff Hasty
Nature Microbiology, 2, 17083 (2017)

Suppression of Beneficial Mutations in Dynamic Microbial Populations

Philip Bittihn, Jeff Hasty, and Lev S. Tsimring
Physical Review Letters, 118 (2017)

Synchronized cycles of bacterial lysis for in vivo delivery

M. Omar Din, Tal Danino, Arthur Prindle, Matt Skalak, Jangir Selimkhanov, Kaitlin Allen, Ellixis Julio, Eta Atolia, Lev S. Tsimring, Sangeeta N. Bhatia, Jeff Hasty
Nature, 536: 81-85 (2016)

Quorum Sensing Communication Modules for Microbial Consortia

Spencer R. Scott and Jeff Hasty
ACS Synthetic Biology, 5(9): 969-977 (2016)

Transcriptional regulation with CRISPR-Cas9: principles, advances, and applications

Criticality and Adaptivity in Enzymatic Networks

Paul J. Steiner, Ruth J. Williams, Jeff Hasty, and Lev S. Tsmimring
Biophysical Journal, 111: 1078-1087 (2016)

Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules

Bartlomiej Borek, Jeff Hasty, Lev Tsimring
PloS One, 11(5): e0153679 (2016)

FBB: A Fast Bayesian Bound tool to calibrate RNA-seq aligners

Irene Rodriguez-Lujan, Jeff Hasty, Ramon Huerta
Bioinformatics, 10.1093/bioinformatics/btw608 (2016)

Programmable probiotics for detection of cancer in urine

Tal Danino, Arthur Prindle, Gabriel A. Kwong, Matthew Skalak, Howard Li, Kaitlin Allen, Jeff Hasty, Sangeeta N. Bhatia
Science Translational Medicine, 7(289), 289ra84 (2015)

A Microfluidic Platform for Long-Term Monitoring of Algae in a Dynamic Environment

Chung Sze Luke, Jangir Selimkhanov, Leo Baumgart, Susan E. Cohen, Susan S. Golden, Natalie A. Cookson, Jeff Hasty
ACS Synthetic Biology, 5:8-14 (2015)

Orthogonal Modular Gene Repression in E. coli Using Engineered CRISPR/Cas9

Andriy Didovyk, Bartlomiej Borek, Jeff Hasty, Lev Tsimring
ACS Synthetic Biology, 5(1): 81-88 (2015)

Distributed Classifier Based on Genetically Engineered Bacterial Cell Cultures

Andriy Didovyk, Oleg I. Kanakov, Mikhail V. Ivanchenko, Jeff Hasty, Ramon Huerta, Lev Tsimring
ACS Synthetic Biology, 4(1): 72-82 (2015)

Rapid and tunable post-translational coupling of genetic circuits

Accurate information transmission through dynamic biochemical signaling networks

Synchronization of Degrade-and-Fire Oscillations via a Common Activator

In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks

Filippo Menolascina, Gianfranco Fiore, Emanuele Orabona, Luca De Stefano, Mike Ferry, Jeff Hasty, Mario di Bernardo, Diego di Bernardo
PloS Computational Biology, 10(5): e1003625 (2014)

Dynamic Localization of the Cyanobacterial Circadian Clock Proteins

Susan E. Cohen, Marcella L. Erb, Jangir Selimkhanov, Guogang Dong, Jeff Hasty, Joe Pogliano, Susan S. Golden
Current Biology, 24(16): 1-9 (2014)

Measuring Competitive Fitness in Dynamic Environments

Ivan A. Razinkov, Bridget L. Baumgartner, MR Bennett, Lev Tsimring, and Jeff Hasty
Journal of Physical Chemistry B, 117:13175-13181 (2013)

Dual Delayed Feedback Provides Sensitivity and Robustness to the NF-kB Signaling Module

Measuring Growth and Gene Expression Dynamics of Tumor-Targeted S.Typhimurium Bacteria

Tal Danino, Arthur Prindle, Jeff Hasty, Sangeeta Bhatia
Journal of Visualized Experiments , e50540-e50540 (2013)

Translational Cross Talk in Gene Networks

William H. Mather, Jeff Hasty, Lev S. Tsimring, and Ruth J. Williams
Biophysical Journal, 104: 2564-2572 (2013)

A sensing array of radically coupled genetic ‘biopixels’

Arthur Prindle, Phillip Samayoa, Ivan Razinkov, Tal Danino, Lev Tsimring, and Jeff Hasty
Nature, 481: 39-44 (2012)

Making gene circuits sing

Arthur Prindle and Jeff Hasty
Proceedings of the National Academy of Sciences, 109(42): 16758-16759 (2012)

In vivo gene expression dynamics of tumor-targeted bacteria

Tal Danino, Justin Lo, Arthur Prindle, Jeff Hasty, and Sangeeta N. Bhatia
ACS Synthetic Biology, 1: 465-470 (2012)

Recent advances in single-cell studies of gene regulation

Vacuum-assisted cell loading enables shear-free mammalian microfluidic culture

Martin Kolnik, Lev Tsimring, and Jeff Hasty
Lab on a Chip, 12(22):4732-7 (2012)

Genetic circuits in Salmonella typhimurium

Arthur Prindle, Jangir Selimkhanov, Tal Danino, Phillip Samayoa, Anna Goldberg, Sangeeta N. Bhatia, and Jeff Hasty
ACS Synthetic Biology, 1: 458-464 (2012)

Fast stochastic algorithm for simulating evolutionary population dynamics

Synthetic biology approaches to biofuel production

Entrainment of a population of synthetic genetic oscillators

Octavio Mondragon-Palomino, Tal Danino, Jangir Selimkhanov, Lev Tsimring, and Jeff Hasty
Science, 333: 1315-1319 (2011)

Queueing up for enzymatic processing: correlated signaling through coupled degradation

Antagonistic gene transcripts regulate adaptation to new growth environments

Bridget L. Baumgartner, Matthew R. Bennett, Michael Ferry, Tracy L. Johnson, Lev S. Tsimring, and Jeff Hasty
Proceedings of the National Academy of Sciences, 1111408109 (2011)

Yeast Dynamically Modify Their Environment to Achieve Better Mating Efficiency

Meng Jin, Beverly Errede, Marcelo Behar, Will Mather, Sujata Nayak, Jeff Hasty, Henrik G. Dohlman, and Timothy C. Elston
Science Signaling, 4(186): ra54 (2011)

In-Silico Patterning of Vascular Mesenchymal Cells in Three Dimensions

Tal Danino, Dmitri Volfson, Sangeeta N. Bhatia, Lev Tsimring, Jeff Hasty
PloS One, 6(5): e20182 (2011)

Microfluidics for synthetic biology: From design to execution

Buckling instability in ordered bacterial colonies

Denis Boyer, William Mather, Octavio Mondragon-Palomino, Sirio Orozco-Fuente, Tal Danino, Jeff Hasty, and Lev Tsimring
Physical Biology, 441:28:00 (2011)

Factorized time-dependent distributions for certain multiclass queueing networks and an application to enzymatic processing network

William H. Mather, Jeff Hasty, Lev S. Tsimring, and Ruth J. Williams
Queueing Systems, 1/16/2011 (2011)

A synchronized quorum of genetic clocks

Tal Danino, Octavio Mondragon-Palomino, Lev Tsimring, Jeff Hasty
Nature, 426: 326-330 (2010)

Streaming Instability in Growing Cell Populations

William Mather, Octavio Mondragon-Palomino, Tal Danino, Jeff Hasty, and Lev S. Tsimring
Physical Review Letters, 104208101 (2010)

Correlation Resonance Generated by Coupled Enzymatic Processing

William H. Mather, Natalie A. Cookson, Jeff Hasty, Lev S. Tsimring, and Ruth J. Wiliams
Biophysical Journal, 99(10) (2010)

Stochastic Emergence of Groupthink

Circadian rhythms in Neurospora crassa: Dynamics of the clock component frequency visualized using a fluorescent reporter

Phenotypic impact of regulatory noise in cellular stress-response pathways

Microfluidic devices for measuring gene network dynamics in single cells

Overpowering the component problem

Cell cycle-dependent variations in protein concentration

The pedestrian watchmaker: Genetic clocks from engineered oscillators

Coherent activation of a synthetic mammalian gene network

Delay-Induced Degrade-and-Fire Oscillations in Small Genetic Circuits

Metabolic gene regulation in a dynamically changing environment

Matthew Bennett, Wyming Lee Pang, Natalie Ostroff, Bridget Baumgartner, Sujata Nayak, Lev Tsimring, Jeff Hasty
Nature, 454(7208):1119-22 (2008)

A fast, robust and tunable synthetic gene oscillator

Systems Biology: Genome rewired

Athermal Dynamics of Strongly Coupled Stochastic Three-State Oscillators

Regulation of Cell Signaling Dynamics by the Protein Kinase-Scaffold Ste5

A molecular noise generator

Biomechanical ordering of dense cell populations

Transient dynamics of genetic regulatory networks

A DNA methylation-based switch generates bistable gene expression

A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae

Phenotypic variability of growing cellular populations

A bottom-up approach to gene regulation

Dynamics of single-cell gene expression

Imaging gene expression: Tiny signals make a big noise

Statistics of cellular signal transduction as a race to the nucleus by multiple random walkers in compartment/phosphorylation space

Effective temperature in stochastic kinetics and gene networks

Stochastically driven genetic circuits

Origins of extrinsic variability in eukaryotic gene expression

Delay-induced stochastic oscillations in gene regulation

Monitoring dynamics of single-cell gene expression over multiple cell cycles

Cellular growth and division in the Gillespie algorithm

Prediction and measurement of an autoregulatory genetic module

Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling

A synthetic gene network for entraining and amplifying cellular oscillations

Design then mutate

Engineered gene circuits

Translating the noise

Synchronizing genetic relaxation oscillators by intercell signalling

Designer gene networks: Towards fundamental cellular control

Computational studies of gene regulatory networks: in numero molecular biology

Protein interactions- Unspinning the web

Wavelets of excitibility in sensory neurons

Complex ligand-protein systems: a globally convergent iterative method for the n x m case

Noise-based switches and amplifiers for gene expression

Renormalization group for directed sandpile models

Renormalization of one-dimensional avalanche models